A framework for human microbiome research

Abstract

A variety of microbial communities and their genes (microbiome) exist throughout the human body, playing fundamental roles in human health and disease. The NIH funded Human Microbiome Project (HMP) Consortium has established a population-scale framework which catalyzed significant development of metagenomic protocols resulting in a broad range of quality-controlled resources and data including standardized methods for creating, processing and interpreting distinct types of high-throughput metagenomic data available to the scientific community. Here we present resources from a population of 242 healthy adults sampled at 15 to 18 body sites up to three times, which to date, have generated 5,177 microbial taxonomic profiles from 16S rRNA genes and over 3.5 Tb of metagenomic sequence. In parallel, approximately 800 human-associated reference genomes have been sequenced. Collectively, these data represent the largest resource to date describing the abundance and variety of the human microbiome, while providing a platform for current and future studies.

An Improved Methodology to Overcome Key Issues in Human Fecal Metagenomic DNA Extraction

“…However, the eubacterial:human ratios were compromised for the fecal metagenomic DNA isolated using commercial methods (2 13 :1 for method A, 2 12 :1 for method B, and 2 0.143 :1 for method C, 2 20.8 :1 for method D). Similar observation on host genomic DNA contamination in fecal metagenomic DNA was recorded during the HMP study using method A [6].…”

“…The total number of microbes residing in the human body, especially in the gut, outnumbers that of human cells [3]. A vast array of recent studies has identified many microbial enterotypes in the human gut [4], [5], [6], [7], [8], [9], [10] and their potential roles in immunity [5], [7], [8], development [8], digestion [9], and other functions [10].…”

“…Many microbes elude complete lysis, resulting in an uneven contribution of metagenomic DNA and eventually compromised microbial diversity [11], [17]. Additionally, human genomic DNA remnants in metagenomic DNA affect the metagenomic sequence data output, thereby increasing per base sequencing cost [6]. To overcome these challenges, many metagenomic DNA extraction protocols are being standardized, which include phenol/chloroform enzymatic lysis and freeze thaw [11], [16], [17], [18], [19], [20], [21], [22].…”

In situ substrate-formed biofilms using IDODS mimic supragingival tooth-formed biofilms

“…This pipeline was applied in the Human Microbiome Project [25]. The sequences were separated using the sample-specific ‘barcodes’.…”

Gas diffusion electrodes improve hydrogen gas mass transfer for a hydrogen oxidizing bioanode

“…Environmental samples were sent to and analysed by GATC Biotech AG (Konstanz, Germany). The microbial community was established by amplicon sequencing of a 570 bp (excluding primer length) fragment of the V3‐V5 hypervariable region 17. PCR amplification was performed by using the 357F (CCTACGGGAGGCAGCAG) and 926R primer (CCGTCAATTCMTTTRAGT).…”